[Rdkit-discuss] Rev. 5775 (Windows) - pyGraphMolWrap test fails
Dear All,
I have just built revision 5775 on Windows, and the pyGraphMolWrap test fails.
The relevant bit of the verbose output is below:
78: ERROR: testGithub498 (__main__.TestCase)
78: --
78: Traceback (most recent call last):
78: File C:/RDKit/Code/GraphMol/Wrap/rough_test.py, line 3033, in
testGithub498
78: outf = gzip.open(tempfile.mktemp(),'wt+')
78: File C:\Anaconda\lib\gzip.py, line 34, in open
78: return GzipFile(filename, mode, compresslevel)
78: File C:\Anaconda\lib\gzip.py, line 94, in __init__
78: fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
78: ValueError: Invalid mode ('wt+b')
This seems to be due to a difference in python/gzip behaviour on Windows vs. eg
Linux:
On Ubuntu (Anaconda python):
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
In [3]:
On Windows (again Anaconda python):
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
---
ValueErrorTraceback (most recent call last)
ipython-input-2-6bee12287576 in module()
1 outf = gzip.open(tempfile.mktemp(), 'wt+')
C:\Anaconda\lib\gzip.pyc in open(filename, mode, compresslevel)
32
33
--- 34 return GzipFile(filename, mode, compresslevel)
35
36 class GzipFile(io.BufferedIOBase):
C:\Anaconda\lib\gzip.pyc in __init__(self, filename, mode, compresslevel,
fileobj, mtime)
92 mode += 'b'
93 if fileobj is None:
--- 94 fileobj = self.myfileobj = __builtin__.open(filename, mode
or 'rb')
95 if filename is None:
96 # Issue #13781: os.fdopen() creates a fileobj with a bogus
name
ValueError: Invalid mode ('wt+b')
In [3]:
Is this an easy one to fix?
Kind regards
James
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Re: [Rdkit-discuss] Rev. 5775 (Windows) - pyGraphMolWrap test fails
Looks like the problem opening the file with the extra parameters used ('t+')
as the gzip module just sticks a 'b' on the end of the opening mode
if mode and 'b' not in mode:
mode += 'b'
The test should run if line 3033 is changed from
outf = gzip.open(tempfile.mktemp(),'wt+')
to
outf = gzip.open(tempfile.mktemp(),'wb+')
which I would put right but I still have zero idea how to use git :)
The more interesting question is why does this work on Unix/Mac but not on
Windows, and why do you get this error when it's not in the gzip code?
Best,
Nick
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On 13 Jul 2015, at 15:16, James Davidson
j.david...@vernalis.commailto:j.david...@vernalis.com wrote:
gzip.pyc
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Re: [Rdkit-discuss] Rev. 5775 (Windows) - pyGraphMolWrap test fails
Just a quick FYI that Paolo's PR has been accepted in github.
I'm still digging out from the email from last week, so I'm slow.
-greg
On Tue, Jul 14, 2015 at 12:23 AM, Paolo Tosco paolo.to...@unito.it wrote:
Hi James,
I just submitted a pull request about this; a patch is attached to this
e-mail. To apply the patch, cd to $RDBASE and issue the following command:
patch -p0 patch20150713.txt
Best,
p.
On 13/07/2015 15:16, James Davidson wrote:
Dear All,
I have just built revision 5775 on Windows, and the pyGraphMolWrap test
fails. The relevant bit of the verbose output is below:
78: ERROR: testGithub498 (__main__.TestCase)
78: --
78: Traceback (most recent call last):
78: File C:/RDKit/Code/GraphMol/Wrap/rough_test.py, line 3033, in
testGithub498
78: outf = gzip.open(tempfile.mktemp(),'wt+')
78: File C:\Anaconda\lib\gzip.py, line 34, in open
78: return GzipFile(filename, mode, compresslevel)
78: File C:\Anaconda\lib\gzip.py, line 94, in __init__
78: fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
78: ValueError: Invalid mode ('wt+b')
This seems to be due to a difference in python/gzip behaviour on Windows
vs. eg Linux:
*On Ubuntu (Anaconda python):*
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
In [3]:
*On Windows (again Anaconda python):*
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
---
ValueErrorTraceback (most recent call last)
ipython-input-2-6bee12287576 in module()
1 outf = gzip.open(tempfile.mktemp(), 'wt+')
C:\Anaconda\lib\gzip.pyc in open(filename, mode, compresslevel)
32
33
--- 34 return GzipFile(filename, mode, compresslevel)
35
36 class GzipFile(io.BufferedIOBase):
C:\Anaconda\lib\gzip.pyc in __init__(self, filename, mode, compresslevel,
fileobj, mtime)
92 mode += 'b'
93 if fileobj is None:
--- 94 fileobj = self.myfileobj = __builtin__.open(filename,
mode or 'rb')
95 if filename is None:
96 # Issue #13781: os.fdopen() creates a fileobj with a
bogus name
ValueError: Invalid mode ('wt+b')
In [3]:
Is this an easy one to fix?
Kind regards
James
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intended for the named addressee(s) only and access to it by anyone else is
unauthorised. If you are not an addressee, any disclosure or copying of the
contents of this email or any action taken (or not taken) in reliance on it
is unauthorised and may be unlawful. If you have received this email in
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a secure method of communication and the Company cannot accept
responsibility for the accuracy or completeness of this message or any
attachment(s). Please check this email for virus infection for which the
Company accepts no responsibility. If verification of this email is sought
then please request a hard copy. Unless otherwise stated, any views or
opinions presented are solely those of the author and do not represent
those of the Company.
The Vernalis Group of Companies
100 Berkshire Place
Wharfedale Road
Winnersh, Berkshire
RG41 5RD, England
Tel: +44 (0)118 938
To access trading company registration and address details, please go to
the Vernalis website at www.vernalis.com and click on the Company
address and registration details link at the bottom of the page..
__
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